Biology subjects

Mazza, F.

Publications and source records attributed to Mazza, F..

12 recordsLinked to original sources

bioRxiv2026

Allele-resolved monosome and polysome sequencing identifies functional cis-acting variants affecting mRNA translation efficiency

To prioritize germline genetic variants affecting mRNA fate at the post-transcriptional and translational levels, we leveraged sucrose-gradient-based isolation of 80S monosomes and polysomes, followed by mRNA retrieval and paired-end sequencing. Total cytoplasmic RNA was also sequenced for comparison. Experiments were performed in the non-transformed cell line RPE-1, cultured under basal conditions or upon p53 activation by Nutlin. Differential gene expression analysis confirmed a canonical p53 response. Heterozygous SNPs and SNVs were identified from the RNA-seq data, and allelic fractions (AF) were calculated for total, monosomal, and polysomal mRNAs. Variants showing reproducible AF differences across fractions beyond experimental variability were defined as tranSNPs. Among nearly 7000 heterozygous variants analyzable in polysomal or total RNA and over 5000 in monosomal mRNA, 1155 displayed a significant imbalance. Reporter assays performed in both RPE-1 and HCT116 cells validated allelic or haplotype effects for 17 selected variants in UTRs and coding regions, confirming differences in 15 cases, with evidence of cell line-specific responses. Proteomic analysis further supported allelic imbalance for selected missense variants. Overall, tranSNPs were identified in a non-transformed cell line at frequencies comparable to those in cancer cells, thereby extending their implications in human physiology. Further, monosome profiling enabled improved detection sensitivity of tranSNPs without positional bias, suggesting that 80S profiling improves detection of allele-specific translational regulation in RPE-1 cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/723424v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@f10281org.highwire.dtl.DTLVardef@db91ccorg.highwire.dtl.DTLVardef@140ea91org.highwire.dtl.DTLVardef@e80c99_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

On the Stability of Silicone-Encapsulated CMOS ICs for Active Implantable Devices: 4.3 Years of Accelerated Life Testing

The reliability of polymer-encapsulated CMOS integrated circuits (ICs) is critical for the development of miniaturised active implantable medical devices (AIMDs). Traditional hermetic packaging methods become impractical as implant sizes decrease, necessitating alternative methods of protection from body fluids. This study evaluates the long-term stability of silicone-encapsulated CMOS ICs through accelerated life testing using electrical impedance spectroscopy (EIS) and visual inspection. CMOS interdigitated combs (IDCs) were encapsulated in medical grade silicone rubber, subjected to immersion in phosphate-buffered saline (PBS), and tested at elevated temperatures (47{degrees}C, 67{degrees}C, and 87{degrees}C) under both 5V DC and biphasic voltage biases for up to 4.3 years. Remarkably, no insulation failures were observed in the IDCs, with no significant water ingress detected through impedance changes. Failures at the ICs were limited to wire bond open-circuits, though there was some pad discolouration/corrosion. Other failures were elsewhere, not at the ICs. This highlights the stability of modern silicon oxide/silicon nitride bilayer passivation when encapsulated in adhesive silicone rubber. Visual analysis revealed occasional solder and aluminium pad corrosion, particularly at higher temperatures, but these changes did not correlate with EIS failures. The findings suggest that silicone encapsulation, combined with passivation and shielding strategies, enables long-term IC reliability in biofluid environments. To our knowledge, this paper presents the longest reported accelerated ageing study of test structures for implantable devices, laying the groundwork for the integration of silicone-encapsulated ICs into next-generation chip-scale bioelectronic implants.

biochemistry↗

bioRxiv2024

A common haplotype in the EXO5 gene can impact its protein structure and dynamics and modulate genome stability and cancer progression

Understanding the impact of common germline variants on protein structure, function, and disease progression is crucial in cancer research. This study presents a comprehensive analysis of the EXO5 gene, which encodes a DNA exonuclease involved in DNA repair previously associated with cancer susceptibility. We employed an integrated approach combining genomic and clinical data analysis, deep learning variant effect prediction, and molecular dynamics simulations to investigate the effects of common EXO5 haplotypes on protein structure, dynamics, and cancer outcomes. We characterized the haplotype structure of EXO5 across diverse human populations, identifying five common haplotypes, and studied their impact on EXO5 protein. Our analyses revealed significant structural and dynamic differences among the EXO5 haplotypes, particularly in their catalytic region. The L151P EXO5 protein variant exhibited the most substantial conformational changes, potentially disruptive for EXO5s function and nuclear localization. Analysis of TCGA data showed that patients carrying L151P EXO5 had significantly shorter progression-free survival in prostate and pancreatic cancers, and exhibited increased genomic instability. This study highlights the strength of our methodology in uncovering the effects of common genetic variants on protein function and their implications for disease outcomes.

bioinformatics↗

bioRxiv2024

Spine loss in depression impairs dendritic signal integration in human cortical microcircuit models

Major depressive disorder (depression) is associated with altered dendritic structure and function in excitatory cortical pyramidal neurons, due to decreased inhibition from somatostatin interneurons and loss of spines and associated synapses, as indicated in postmortem human studies. Dendrites play an important role in signal processing as they receive the majority of synaptic inputs and exhibit nonlinear properties including backpropagating action potentials and dendritic Na+ spikes that enhance the computational power of the neuron. However, it is currently unclear how depression-related dendritic changes impact the integration of signals. Here, we expanded our previous data-driven detailed computational models of human cortical microcircuits in health and depression to include active dendritic properties that enable backpropagating action potentials as measured in human neurons, and spine loss in depression in terms of synapse loss and altered intrinsic property. We show that spine loss dampens signal response and thus results in a larger impairment of cortical function such as signal detection than due to reduced somatostatin interneuron inhibition alone. We further show that the altered intrinsic properties due to spine loss abolish nonlinear dendritic integration of signals and impair recurrent microcircuit activity. Our study thus mechanistically links cellular changes in depression to impaired dendritic processing in human cortical microcircuits.

neuroscience↗

bioRxiv2024

Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity

Treatment for major depressive disorder (depression) often has partial efficacy and a large portion of patients are treatment resistant. Recent studies implicate reduced somatostatin (SST) interneuron inhibition in depression, and new pharmacology boosting this inhibition via positive allosteric modulators of 5-GABAA receptors (5-PAM) offers a promising effective treatment. However, testing the effect of 5-PAM on human brain activity is limited, meriting the use of detailed simulations. We utilized our previous detailed computational models of human depression microcircuits with reduced SST interneuron inhibition and 5-PAM effects, to simulate EEG of virtual subjects across depression severity and 5-PAM doses. We developed machine learning models that predicted optimal dose from EEG with high accuracy and recovered microcircuit activity and EEG. This study provides dose prediction models for 5-PAM administration based on EEG biomarkers of depression severity. Given limitations in doing the above in the living human brain, the results and tools we developed will facilitate translation of 5-PAM treatment to clinical use.

neuroscience↗

bioRxiv2024

EEG biomarkers of GABA α5 positive allosteric modulators in rodents

Reduced cortical inhibition mediated by gamma-aminobutyric acid (GABA) is reported in depression, anxiety disorders, and aging. Novel positive allosteric modulator that specifically target 5-GABAA receptor subunit (5-PAM), ligand GL-II-73, shows anxiolytic, antidepressant, and pro-cognitive effects without the common side effects associated with non-specific modulation by benzodiazepines such as diazepam (DZP), thus suggesting novel therapeutic potential. However, it is unknown if 5-PAM has detectable signatures in clinically-relevant brain electroencephalography (EEG). We analyzed EEG in freely moving rats at baseline and following injections of 5-PAM and DZP. We showed that 5-PAM specifically decreased theta peak power whereas DZP shifted peak power from high to low theta, while increasing beta and gamma power. EEG decomposition showed that these effects were periodic and corresponded to changes in theta oscillation event duration. Our study thus shows that 5-PAM has robust and distinct EEG biomarkers in rodents, indicating that EEG could enable non-invasive monitoring of 5-PAM treatment efficacy.

neuroscience↗

bioRxiv2024

Longevity of Implantable Silicon-ICs for Emerging Neural Applications: Evaluation of Bare Die and PDMS-Coated ICs After Accelerated Aging and Implantation Studies

Silicon integrated circuits (ICs) are central to the next-generation miniature active neural implants, whether packaged in soft polymers for flexible bioelectronics or implanted as bare die for neural probes. These emerging applications bring the IC closer to the corrosive body environment, raising reliability concerns, particularly for long-term clinical use. Here, we evaluated the long-term electrical and material stability of silicon-ICs from two foundries, after one-year accelerated in vitro and in vivo animal studies. The ICs featured various custom-designed test structures and were partially PDMS coated, creating two regions on each chip, uncoated "bare die" and "PDMS-coated". During the accelerated in vitro study, ICs were electrically biased and periodically monitored. Results demonstrated stable electrical performance for at least a year, suggesting that bare die ICs can function in the body for months. Despite electrical stability, material analysis revealed chemical and electrically driven degradation of the IC passivation in the bare die regions. In contrast, PDMS-coated regions revealed no such degradation, making PDMS a highly suitable encapsulant for ICs intended for years-long implantation. Based on the new insights, guidelines are proposed that may enhance the longevity of implantable ICs, significantly broadening their applications in the biomedical field.

neuroscience↗

bioRxiv2023

Implications of reduced inhibition in schizophrenia on simulated human prefrontal microcircuit activity and EEG

Reduced cortical inhibition by parvalbumin-expressing (PV) interneurons in schizophrenia is thought to be associated with impaired cortical processing in the prefrontal cortex and altered EEG signals such as oddball mismatch negativity (MMN). Recent studies also suggest loss of somatostatin (SST) interneuron inhibition. However, establishing the link between reduced interneuron inhibition and reduced MMN experimentally in humans is currently not possible. To overcome these challenges, we simulated spiking activity and EEG during baseline and oddball response in detailed models of human prefrontal microcircuits in health and schizophrenia, with reduced PV and SST interneuron inhibition as constrained by postmortem patient data. We showed that reduced PV interneuron inhibition can account for the decreased MMN amplitude seen in schizophrenia, with a threshold below which the amplitude effect was low as seen in at-risk patients. In contrast, reduced SST interneuron inhibition did not affect the MMN amplitude. We further showed that both types of inhibition loss were necessary to account for changes in resting EEG in schizophrenia, with reduced SST interneuron inhibition increasing theta power, and reduced PV interneuron inhibition leading to a right shift from alpha to beta frequencies. Our study thus links reduced PV and SST interneuron inhibition in schizophrenia to distinct EEG biomarkers that can serve to improve stratification and early detection using non-invasive brain signals.

neuroscience↗

bioRxiv2023

In-silico testing of new pharmacology for restoring inhibition and human cortical function in depression

Reduced inhibition by somatostatin-expressing interneurons is associated with depression. Administration of positive allosteric modulators of 5 subunit-containing GABAA receptor (5-PAM) that selectively target this lost inhibition exhibit antidepressant and pro-cognitive effects in rodent models of chronic stress. However, the functional effects of 5-PAM on the human brain in vivo are unknown, and currently cannot be assessed experimentally. We modeled the effects of 5-PAM on tonic inhibition as measured in human neurons, and tested in silico 5-PAM effects on detailed models of human cortical microcircuits in health and depression. We found that 5-PAM effectively recovered impaired cortical processing as quantified by stimulus detection metrics, and also recovered the power spectral density profile of the microcircuit EEG signals. We performed an 5-PAM dose response and identified simulated EEG biomarker candidates. Our results serve to de-risk and facilitate 5-PAM translation and provide biomarkers in non-invasive brain signals for monitoring target engagement and drug efficacy.

neuroscience↗

bioRxiv2021

EEG Biomarkers of reduced inhibition in human cortical microcircuits in depression

Reduced cortical inhibition by somatostatin-expressing (SST) interneurons has been strongly associated with treatment-resistant depression. However, whether the effects of reduced SST interneuron inhibition on microcircuit activity have signatures detectible in electroencephalography (EEG) signals remains unknown. We simulated resting-state activity and EEG using detailed models of human cortical microcircuits with normal (healthy) or reduced SST interneuron inhibition (depression). Healthy microcircuit models showed emergent key features of resting-state EEG, and depression microcircuits exhibited increased theta, alpha and low beta power (4 - 15 Hz). The changes in depression involved a combination of an aperiodic broadband, and periodic theta components. We then demonstrated the specificity of the EEG signatures of reduced SST interneuron inhibition by showing they were distinct from those corresponding to reduced parvalbumin-expressing (PV) interneuron inhibition. Our study thus links SST interneuron inhibition level to distinct features in EEG simulated from detailed human microcircuits, which can serve to better identify mechanistic subtypes of depression using EEG, and non-invasively monitor modulation of cortical inhibition.

neuroscience↗

bioRxiv2021

Mapping inter-individual functional connectivity variability in TMS targets for major depressive disorder

Transcranial magnetic stimulation (TMS) is an emerging alternative to existing treatments for major depressive disorder (MDD). The effects of TMS on both brain physiology and therapeutic outcomes are known to be highly variable from subject to subject, however. Proposed reasons for this variability include individual differences in neurophysiology, in cortical geometry, and in brain connectivity. Standard approaches to TMS target site definition tend to focus on coordinates or landmarks within the individual brain regions implicated in MDD, such as the dorsolateral prefrontal cortex (dlPFC) and orbitofrontal cortex (OFC). Additionally considering the network connectivity of these sites has the potential to improve subject-specificity of TMS targeting and, in turn, improve treatment outcomes. We looked at the functional connectivity (FC) of dlPFC and OFC TMS targets, based on induced electrical field (E-field) maps, estimated using the SimNIBS library. We generated individualized E-field maps on the cortical surface for 121 subjects from the Human Connectome Project database using tetrahedral head models generated from T1-weighted MR images. We analyzed inter-subject variability in the shape and location of these TMS target E-field patterns, their FC, and the major functional networks to which they belong. Our results revealed the key differences in TMS target FC between the dlPFC and OFC, and also how this connectivity varies across subjects. Three major functional networks were targeted across the dlPFC and OFC: the ventral attention, fronto-parietal and default-mode networks in the dlPFC, and the fronto-parietal and default mode networks in the OFC. Inter-subject variability in cortical geometry and in FC was high. Our results characterize the FC patterns of canonical therapeutic TMS targets, and the key dimensions of their variability across subjects. The high inter-individual variability in cortical geometry and FC, leading to high variability in distributions of targeted brain networks, may account for the high levels of variability in physiological and therapeutic TMS outcomes. These insights should, we hope, prove useful as part of the broader effort by the psychiatry, neurology, and neuroimaging communities to help improve and refine TMS therapy, through a better understanding of the technology and its neurophysiological effects. HighlightsO_LIE-field modelling and functional connectivity used to study TMS targets (dlPFC,OFC) C_LIO_LIConsiderable variability in TMS target E-field patterns seen across subjects C_LIO_LILarge inter-subject differences in target connectivity observed and characterized C_LIO_LIMajor functional networks targeted by dlPFC, OFC TMS were the VAN, FPN and DMN C_LIO_LIInsights can contribute to improved and more personalized TMS therapies in the future C_LI

neuroscience↗

bioRxiv2021

Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits

Cortical processing depends on finely-tuned excitatory and inhibitory connections in neuronal microcircuits. Reduced inhibition by somatostatin-expressing interneurons is a key component of altered inhibition associated with treatment-resistant major depressive disorder (depression), which is implicated in cognitive deficits and rumination, but the link remains to be better established mechanistically in humans. Here, we tested the impact of reduced somatostatin interneuron mediated inhibition on cortical processing in human neuronal microcircuits using a data-driven computational approach. We integrated human cellular, circuit and gene-expression data to generate detailed models of human cortical microcircuits in health and depression. We simulated microcircuit baseline and response activity and found reduced signal-to-noise ratio and increased false/failed detection of stimuli due to a higher baseline activity in depression. Our results thus applied novel models of human cortical microcircuits to demonstrate mechanistically how reduced inhibition impairs cortical processing in depression, providing quantitative links between altered inhibition and cognitive deficits.

neuroscience↗